Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization.

Quality Control and Peak Finding for Proteomics Data Collected from Nipple Aspirate Fluid Using Surface Enhanced Laser Desorption and Ionization

Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform.

Mass spectrometry is being used to find disease-related patterns in mixtures of proteins derived from biological fluids. Questions have been raised about the reproducibility and reliability of peak quantifications using this technology. We collected nipple aspirate fluid from breast cancer patients and healthy women, pooled them into a quality control sample, and produced 24 replicate SELDI spe...

Proteomic Patterns of Nipple Aspirate Fluids Obtained by SELDI-TOF: Potential for New Biomarkers to Aid in the Diagnosis of Breast Cancer

Nipple aspirate fluid (NAF) has been used for many years as a potential non-invasive method to identify markers for breast cancer risk or early detection. Because individual markers have not been optimal, we are exploring the use of surface enhanced laser desorption and ionization time of flight (SELDI-TOF) mass spectrometry to identify patterns of proteins that might define a proteomic signatu...

Detection of breast cancer biomarkers in nipple aspirate fluid by SELDI-TOF and their identification by combined liquid chromatography-tandem mass spectrometry.

Screening mammography is the most effective tool available for breast cancer detection. While screening mammography saves lives, it has intrinsic problems that limit further improvement. We hypothesize that protein biomarkers in nipple aspirate fluid (NAF) may separate the cancer from the non-cancer state, and therefore can be used for breast cancer detection. In this study the proteins in NAF ...

Cancer Classification Using Mass Spectrometry-based Proteomics Data

This document presents data analysis similar to Wang (2011) using R package bst. Serum samples were collected from 77 benign prostate hyperplasia (BPH), 84 early stage prostate cancer, 83 late stage prostate cancer and 82 age-matched healthy men (HM). Peak detection and alignment were based on surface-enhanced laser desorption/ionization (SELDI) mass spectrometry protein profiles. The data have...